Computational Molecular Biology (Spring

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Computational Molecular Biology (Spring03)

• Chitta Baral
• Professor of Computer Science Engg.
• http//www.public.asu.edu/cbaral

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Introduction

• Biology
• The science of life that branch of knowledge
  which treats of living matter as distinct from
  matter which is not living the study of living
  tissue. It has to do with the origin, structure,
  development, function, and distribution of
  animals and plants.
• Molecular
• Pertaining to, connected with, produced by, or
  consisting of, molecules
• Molecule the simplest structural unit of an
  element or compound
• Computational
• of or involving computation or computers
• Computational Molecular Biology Application of
  computation and computers in the study of biology
  (the science of life) at the molecular level.

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Molecular Biology issues of interest

• Studying the interaction of molecules in an
  organism.
• Some important molecules in an organism
• Sugar, carbohydrates
• Proteins (made up of aminoacids)
• E.g. Enzymes
• Fats (lipids)
• Oxygen (O2)
• Acids (Deoxyribo Nucleic Acids)
• Alcohols

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CMB and health, diseases and disorders

• The source of diseases and disorders can often be
  traced to activities inside cells.
• The activities inside cells are often regulated
  by proteins (enzymes, ligands on cell surfaces,
  etc.)
• Central Dogma DNA ? RNA ? Proteins
• The presence, absence and concentration of
  particular proteins inside cells are related to
  the expression of the genes that play a role in
  producing those proteins or in producing related
  proteins which help in transforming to/from these
  proteins.
• Need to know which genes play a role in
  production of which proteins.
• Need to know which genes are located where, and
  what is the DNA sequence of that gene.
• How do we figure out what (various interacting
  chain of reactions/events -- pathways) is
  happening inside a cell?
• If we suspect or guess of a particular reaction,
  or a set of reactions we can set up experiments
  to verify if indeed that is happening. But how do
  we guess?
• Do micro-array experiments to study the gene
  expression (i.e., which genes are active).
• By looking at the database of the same gene or
  similar (homologous) genes we can try to find out
  what is known about those genes in terms of their
  function (what proteins they produce)
• From the information obtained and from knowledge
  about biochemistry we can make some guesses about
  particular reactions.
• From guesses about particular reactions we try to
  guess about particular pathways.

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CMB some active research issues

• Finding Genomes (gene sequencing)
• Human genome (substantially completed)
• 3 billion base pairs in 46 chromosomes.
• Computing techniques are very important here.
• Matching DNA sequences (algorithms)
• Genes to phenotypes (Linkage analysis)
• Relate genes to phenotypes (externally observable
  traits) by analyzing genomes of a family or over
  a population
• Gene expression to pathways (dynamics of a cell)
• Analyzing micro-array data (data mining,
  clustering)
• Knowledge gathering, automatic annotation (from
  the literature)
• Data and Knowledge integration across databases
• Pathways prediction and analysis (reasoning about
  actions and events)
• Drug design (AI planning) to modify the dynamics
  of the cell.
• Phylogeny
• Relating genes within and across species to
  understand their evolutionary relationship.
• Prediction of secondary structure of proteins
  from their primary structure